Ancient Hominin Species Interbred with an Unknown Hominin Species – Surprising DNA Analysis

Researchers have pieced together the oldest human DNA sequence ever recovered from the fossil record after extracting genetic material from the thigh bone of an ancient hominin who lived 400,000 years ago. The DNA study has added to the mystery of early human evolution, it suggests that our family tree was somewhat more crowded than previously suspected. The femur (thigh bone) found in Spain, suggests that this early human was related to a species of hominin known from a few fragments of fossil material found in Siberia (Denisova hominin). In 2010, scientists discovered evidence of a species of human, perhaps a sub-species of H. sapiens, or an entirely different branch of the human family tree in the Denisova Caves in the remote Altai Mountains (Siberia).

The surprising result poses a puzzle for palaeoanthropologists because it shows that the humans living in northern Spain, where the femur fossil was found, share aspects of their DNA with another type of human that is known to have lived 5,000 miles away. The femur and the DNA contained within it belong to a type of human that pre-dates our own species. Fossils have been found in large numbers at La Sima de los Huesos – the “bone pit”, in the caves of Atapuerca (northern Spain). The cave system, a UNESCO World Heritage site, has yielded at least two dozen skeletons, it seems likely that these ancient humans may have deliberately placed bodies of their clan members in the caves. Although this species has been classified as the robust, six foot plus, H. heidelbergensis, studies also show that these people had some Neanderthal (Homo neanderthalensis) characteristics. Indeed, it has been suggested by some scientists that the fossil bones represent a group of early Neanderthals, as it is believed that H. neanderthalensis evolved from H. heidelbergensis.

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The thigh bone enabled the research team to sequence almost the complete genome from the creature’s mitochondria (part of the cell that is responsible for the production of energy). Mitochondrial DNA (mtDNA) is passed down the maternal line and this makes it extremely valuable when it comes to tracking evolutionary lineages. Once analysed, the mtDNA suggested a link between this Spanish population and the Denisovans. This came as a huge surprise to the researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, (Germany).

Scientists know that around 40,000 years ago three types of human existed in Europe/Siberia, our species (H. sapiens), the Neanderthals and the Denisovans. It is possible, that all three types of humans interbred. The research, led by Matthias Meyer has been published in the academic journal “Nature”.

Professor Chris Stringer, an expert on human evolution at the Natural History Museum (London), commented:

“This unusual finding could be due to at least two different scenarios, both relating to the maternal inheritance of mtDNA and the ease with which it can be lost in a lineage. One scenario is that the mtDNA is derived from an ancient population, ancestral to both the Sima fossil population and Denisovans, which has since been lost in lineages in Africa and Western Eurasia. A second, is that ancestral species interbred in Eurasia, passing over distinctive mtDNA which may have been lost later in the Neanderthal lineage, yet retained in the Denisovan branch”.

The study of genetic material from ancient hominins is opening up a whole new area of study for palaeoanthropologists. The analysis of 400,000 year old mtDNA is helping scientists to gain a better understanding of the complex origins of our own species and the connections between other types of ancient human.

Professor Stringer added:

“Either way, this new finding can help us start to disentangle the relationships of the various human groups known from the last 600,000 years. If more mtDNA can be recovered from the Sima ‘population’ of fossils, it may demonstrate how these individuals were related to each other, and how varied their population was. Additionally, the recovery of such ancient DNA means that other human fossils from this time period can now be considered for DNA analysis.”

The mtDNA was extracted from just two grammes of powdered fossil bone taken from the femur. Once the genetic information had been isolated and sequenced it was compared to extant simians, our own genome and the genome of the Neanderthal plus genetic data from Denisovan fossil material. Although this technique is destructive, only minute amounts of fossil material are needed, but it is important to ensure no contamination of the sample occurs. Thanks to this study, the researchers have revealed that at least one member of the ancient hominin Spanish population shared a 700,000 year old common ancestor with the hominins that were present in the Altai Mountains of Siberia (Denisovans).

Dr. Meyer stated:

“The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neanderthal mtDNA is unexpected because its skeletal remains carry Neanderthal-derived features.”

“Our results show that we can now study DNA from human ancestors that are hundreds of thousands of years old. This opens prospects to study the genes of the ancestors of Neanderthals and Denisovans. It is tremendously exciting.”

It seems that the branch of evolution that led to the hominins and ultimately to us is a little more complicated than previously thought. However, new techniques of genetic data recovery and analysis will in the future unlock the secrets of our ancestry. We can expect one or two more surprises in store.